[med-svn] [salmon] 03/09: Merge tag 'upstream/0.7.1+ds1'
Andreas Tille
tille at debian.org
Tue Aug 30 10:12:29 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository salmon.
commit c6c13cb2aab45dfd0583bc3b74f6b59cb1dd5e04
Merge: a9ee4aa 8a4ec88
Author: Andreas Tille <tille at debian.org>
Date: Tue Aug 30 11:04:23 2016 +0200
Merge tag 'upstream/0.7.1+ds1'
Upstream version 0.7.1+ds1
.clang-format | 94 +
.gitignore | 3 +
CMakeLists.txt | 195 +-
README.md | 12 +-
cmake/Modules/FindJellyfish.cmake | 26 +
cmake/PostInstall.cmake | 12 +-
cmake/TestSalmon.cmake | 35 -
cmake/TestSalmonFMD.cmake | 33 +
cmake/TestSalmonQuasi.cmake | 24 +
cmake/UnitTests.cmake | 10 +
doc/source/ReadLibraryIllustration.png | Bin 43418 -> 169638 bytes
doc/source/conf.py | 18 +-
doc/source/file_formats.rst | 182 +
doc/source/index.rst | 1 +
doc/source/library_type.rst | 2 +-
doc/source/sailfish.rst | 89 -
doc/source/salmon.rst | 500 +-
docker/Dockerfile | 28 +
docker/build_test.sh | 2 +
external/.gitignore | 28 -
include/AlignmentGroup.hpp | 2 +-
include/AlignmentLibrary.hpp | 167 +-
include/BAMQueue.hpp | 9 +-
include/BAMQueue.tpp | 33 +-
include/BWAMemStaticFuncs.hpp | 120 +
include/BWAUtils.hpp | 34 +
include/BiasParams.hpp | 43 +
include/BootstrapWriter.hpp | 15 +
include/ClusterForest.hpp | 5 +-
include/CollapsedEMOptimizer.hpp | 11 +
include/CollapsedGibbsSampler.hpp | 5 +-
include/DistributionUtils.hpp | 66 +
include/EquivalenceClassBuilder.hpp | 94 +-
include/FASTAParser.hpp | 4 +-
include/FastxParser.hpp | 150 +
include/ForgettingMassCalculator.hpp | 2 +-
include/FragmentLengthDistribution.hpp | 9 +
include/FragmentStartPositionDistribution.hpp | 25 +-
include/GCFragModel.hpp | 181 +
include/GZipWriter.hpp | 57 +
include/IndexVersionInfo.hpp | 11 +
include/KmerContext.hpp | 39 +
include/KmerIntervalMap.hpp | 131 +
include/LibraryFormat.hpp | 84 +-
include/LibraryTypeDetector.hpp | 153 +
include/LightweightAlignmentDefs.hpp | 1497 ++++
include/MultinomialSampler.hpp | 104 +-
include/PCA.hpp | 8 +-
include/PairSequenceParser.hpp | 12 +-
include/ReadExperiment.hpp | 507 +-
include/ReadKmerDist.hpp | 79 +
include/ReadLibrary.hpp | 66 +-
include/ReadPair.hpp | 46 +-
include/SBModel.hpp | 90 +
include/SGSmooth.hpp | 13 +
include/SalmonConfig.hpp | 7 +-
include/SalmonIndex.hpp | 364 +
include/SalmonIndexVersionInfo.hpp | 80 +
include/SalmonMath.hpp | 31 +
include/SalmonOpts.hpp | 73 +-
include/{SpinLock.hpp => SalmonSpinLock.hpp} | 6 +-
include/SalmonUtils.hpp | 110 +-
include/Sampler.hpp | 39 +-
include/SimplePosBias.hpp | 43 +
include/TextBootstrapWriter.hpp | 101 +
include/Transcript.hpp | 402 +-
include/TranscriptCluster.hpp | 5 +-
include/TryableSpinLock.hpp | 25 +
include/UnpairedRead.hpp | 14 +
include/UtilityFunctions.hpp | 160 +
include/blockingconcurrentqueue.h | 981 +++
include/concurrentqueue.h | 1236 ++--
include/cuckoohash_config.h | 16 -
include/cuckoohash_config.hh | 34 +
include/cuckoohash_map.hh | 2652 +++----
include/cuckoohash_util.h | 23 -
include/cuckoohash_util.hh | 177 +
include/default_hasher.hh | 29 +
include/kseq.h | 235 -
include/lazy_array.hh | 119 +
include/make_unique.hpp | 45 +
include/posix.h | 344 -
include/spline.h | 404 ++
include/tensemble/BaseForest.h | 513 --
include/tensemble/BaseGBM.h | 426 --
include/tensemble/ClassificationCriterion.h | 201 -
include/tensemble/Criterion.h | 163 -
include/tensemble/Estimator.h | 79 -
include/tensemble/EvaluateMetric.h | 83 -
include/tensemble/FeatureData.h | 227 -
include/tensemble/GBMClassifier.h | 400 --
include/tensemble/GBMRegressor.h | 242 -
include/tensemble/LossFunction.h | 350 -
include/tensemble/RandomForestClassifier.h | 269 -
include/tensemble/RandomForestRegressor.h | 279 -
include/tensemble/RandomGenerator.h | 33 -
include/tensemble/ReadData.h | 163 -
include/tensemble/Tree.h | 731 --
include/tensemble/Tree.h.backup.h | 391 -
include/tensemble/TreeClassifier.h | 74 -
include/tensemble/TreeNode.h | 41 -
include/tensemble/TreeRegressor.h | 66 -
include/tensemble/TypeDef.h | 39 -
include/tensemble/cmdline.h | 160 -
include/xxhash.h | 196 +
scripts/ConvertBootstrapsToTSV.py | 95 +
scripts/compile.sh | 36 +
scripts/cpld.bash | 35 -
scripts/fetchRapMap.sh | 37 +
scripts/make-release.sh | 2 +-
scripts/runner.sh | 24 +
src/BWAUtils.cpp | 146 +
src/BiasCorrectionDriver.cpp | 52 -
src/BuildSalmonIndex.cpp | 237 +-
src/CMakeLists.txt | 239 +-
src/CollapsedEMOptimizer.cpp | 1280 +++-
src/CollapsedGibbsSampler.cpp | 229 +-
src/ComputeBiasFeatures.cpp | 225 -
src/DistributionUtils.cpp | 89 +
src/FASTAParser.cpp | 40 +-
src/FastxParser.cpp | 306 +
src/FragmentLengthDistribution.cpp | 23 +-
src/FragmentStartPositionDistribution.cpp | 128 +-
src/GZipWriter.cpp | 424 ++
src/PerformBiasCorrection.cpp | 349 -
src/PerformBiasCorrection_old.cpp | 420 --
src/SBModel.cpp | 295 +
src/SGSmooth.cpp | 555 ++
src/Salmon.cpp | 32 +-
src/SalmonQuantify.cpp | 5174 ++++++--------
src/SalmonQuantifyAlignments.cpp | 986 ++-
src/SalmonUtils.cpp | 3845 +++++++---
src/SequenceBiasModel.cpp | 3 +-
src/SimplePosBias.cpp | 78 +
src/TranscriptGroup.cpp | 7 +-
src/cokus.cpp | 196 -
src/merge_files.cc | 149 -
src/posix.cc | 252 -
src/xxhash.c | 915 +++
tests/GCSampleTests.cpp | 61 +
tests/KmerHistTests.cpp | 137 +
tests/LibraryTypeTests.cpp | 166 +
tests/UnitTests.cpp | 13 +
tests/catch.hpp | 9416 +++++++++++++++++++++++++
144 files changed, 30021 insertions(+), 14722 deletions(-)
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